Related papers: Sequence alignment and mutual information
One of the main problems that emerges in the classic approach to semantics is the difficulty in acquisition and maintenance of ontologies and semantic annotations. On the other hand, the Internet explosion and the massive diffusion of…
A variety of methods have been proposed for structure similarity calculation, which are called structure alignment or superposition. One major shortcoming in current structure alignment algorithms is in their inherent design, which is based…
Bioinformatics, which is now a well known field of study, originated in the context of biological sequence analysis. Recently graphical representation takes place for the research on DNA sequence. Research in biological sequence is mainly…
We propose a fully data-driven approach to designing mutual information (MI) estimators. Since any MI estimator is a function of the observed sample from two random variables, we parameterize this function with a neural network (MIST) and…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Sequence alignment forms the basis of many methods for functional annotation by phylogenetic comparison, but becomes unreliable in the `twilight' regions of high sequence divergence and short gene length. Here we perform a cross-species…
In many applications involving multi-media data, the definition of similarity between items is integral to several key tasks, e.g., nearest-neighbor retrieval, classification, and recommendation. Data in such regimes typically exhibits…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
Measuring Mutual Information (MI) between high-dimensional, continuous, random variables from observed samples has wide theoretical and practical applications. Recent work, MINE (Belghazi et al. 2018), focused on estimating tight…
Estimating mutual correlations between random variables or data streams is essential for intelligent behavior and decision-making. As a fundamental quantity for measuring statistical relationships, mutual information has been extensively…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
Recent advances in large language models (LLMs) have revolutionized natural language processing, yet evaluating their intrinsic linguistic understanding remains challenging. Moving beyond specialized evaluation tasks, we propose an…
Estimation of mutual information between (multidimensional) real-valued variables is used in analysis of complex systems, biological systems, and recently also quantum systems. This estimation is a hard problem, and universally good…
Motivation: With the rapid expansion of large-scale biological datasets, DNA and protein sequence alignments have become essential for comparative genomics and proteomics. These alignments facilitate the exploration of sequence similarity…
A wide range of tasks in network analysis, such as clustering network populations or identifying anomalies in temporal graph streams, require a measure of the similarity between two graphs. To provide a meaningful data summary for…
The comparison of alternative rankings of a set of items is a general and prominent task in applied statistics. Predictor variables are ranked according to magnitude of association with an outcome, prediction models rank subjects according…
While increasingly complex approaches to question answering (QA) have been proposed, the true gain of these systems, particularly with respect to their expensive training requirements, can be inflated when they are not compared to adequate…
A computational framework utilizes the traditional similarity measures for mining the significant relationships in biological annotations is recently proposed by Tatiana V. Karpinets et al. [2]. In this paper, an improved approximation…
Mutual information has many applications in image alignment and matching, mainly due to its ability to measure the statistical dependence between two images, even if the two images are from different modalities (e.g., CT and MRI). It…